A microscope system includes: a light source unit that emits linear illumination parallel to a first direction; an objective lens that condenses the linear illumination onto a measurement target region; an acquisition unit that acquires a first optical signal indicating a light intensity value of light emitted from the measurement target region by the linear illumination; and a focus control unit that controls at least one of a relative position or a relative posture of the light source unit and an imaging unit that generates the first optical signal on a basis of a light intensity distribution of the first optical signal.